Objective To study the effect of prolonged perioperative use of low molecular weight heparin on progression free survival (PFS) after resection of colon cancer. Methods A total of 214 patients with stageⅠand stage Ⅱ colon cancer who underwent surgery in the People’s Hospital of Yuhuan from January 2015 to December 2017 were selected and divided into group A (n=107) and group B (n=107) according to random number table method. PFS, the incidence of postoperative deep venous thrombosis (DVT) and the related indexes of operation, preoperative and postoperative coagulation function [prothrombin time (PT), partially activated prothrombin time (APTT), fibrinogen (FIB) and D-dimer (D-D)] were compared in the two groups. Results The median PFS in group B was higher than that in group A, and the difference was statistically significant (P<0.05). There was no significant difference in operation time, intraoperative bleeding, exhaust time and hospitalization time between the two groups (P>0.05). 1 day and 3 days after operation, PT and APTT in two groups were lower than those before operation, FIB and D-D were higher than those before operation, and the differences were statistically significant (P<0.05). 3 days after operation, PT and APTT in the two groups were higher than those in 1 day after operation, and FIB and D-D were lower than those in 1 day after operation. The differences were statistically significant (P<0.05). There was no significant difference between the two groups during hospitalization, after discharge and the total symptomatic DVT (P>0.05). The incidence of asymptomatic DVT in group B was significantly lower than that in group A (P<0.05). Conclusion Prolonging the use of low molecular weight heparin after radical resection of colon cancer can reduce the occurrence of asymptomatic DVT and improve PFS, which is worthy of further clinical research.